Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication

Abstract

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.

Differences in rhizosphere soil fungal communities of wild and cultivated Paeonia ludlowii species

“…Although there was little difference between Pathotrophs in the wild and cultivated species, the Soil Saprotroph of LCT2 was significantly higher than that of LZT2, and the Mixed Saprotroph of LCT1 was significantly higher than that of LZT1. These Saprotrophs are prone to enrichment in decaying and diseased plants and are more prone to causing plant diseases ( Zhang et al., 2022 ). Rhizosphere soil fungi and bacteria exhibited similar patterns, compared to cultivated varieties, wild beet ( Beta vulgaris ssp.)…”

The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding

“…Moreover, plant genotype has a significant effect on rhizosphere microbial communities [ 37 ] and the artificial selection of plant host genomes during domestication could affect their interaction with AMF or other soil microorganisms [ 38 ]. Whether modern crop varieties lost the genes required to benefit from mutualistic interactions will be interesting to study using large sequence databases [ 33 ].…”

Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice

“…However, recent studies revealed that during the process of domestication, crop plants may not only lose genetic diversity, but also lose some host-specific microbes, which may be recruited by the distinct traits of wild relatives ( 14 , 19 ). So far, the rhizosphere microbial communities of wild rice have been preliminarily characterized ( 20 ), while the phyllosphere microbiome of wild rice has rarely been documented. Therefore, it is crucial to gain a better understanding of the phyllosphere microbial community of wild rice, which is also essential to modulate its activity for the benefit of rice production.…”